Gut Health Secrets with Vincent Pedre, MD

Content By: Ari Whitten & Dr. Vincent Pedre

In this double podcast release, I am speaking with Dr. Vincent Pedre about his new book GutSMART and his protocol for solving gut issues.

Table of Contents

In this first episode, Dr. Pedre and I discuss:

  • The value of testing for gut issues. (I relate an almost unbelievable tale about my quest to check these kinds of tests for consistency and accuracy.)
  • The possibility of diagnosing and treating your gut symptoms (the concept advanced in Dr. Pedre’s new book)
  • Why Dr. Pedre personally analyzed the gut biome of Hadza hunter-gatherers in his efforts to solve the riddle of modern gut problems
  • The crucial role of a diverse gut microbiome and the decline of microbial variety in the Western diet during the 21st Century
  • What recent studies suggest is the better approach for microbiome diversity and fighting inflammation – a high-fiber diet or one rich in fermented foods?
  • The foods and drugs that can destroy gut diversity, cause leaky gut, create inflammation, and finally wreak havoc on your mitochondria
  • Why a high fiber (or prebiotic) intake in a gut with low flora diversity may worsen symptoms for some people (at least temporarily)
  • A potential solution for those who get bloating and gas when they introduce more prebiotics foods or resistant starch into their diet

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Ari: Dr. Pedre, welcome back to the show for the second time in less than a year. You are a madman in the sense that you have now produced another book on gut health. First of all, you’re meaning madman in the sense of being a prolific content creator and author.

Dr. Vincent Pedre: I think you could say madman also for writing a second book. Look at you, you’re a book author, and I don’t know that people really understand the amount of work that it takes to put a book that they hold in their hands and very quickly browse through. There’s no part of the book that is unintentional.

Ari: Yes, I’m writing—

Dr. Pedre: Every single piece.

Ari: I’m writing my next book right now, and I have a deadline in a few months, and I’ve spent the last three weeks just writing one chapter. Just trying to get this one chapter to a place where I’m really happy with it. There is no doubt that it’s, I think, a massive amount of work and way more so than people realize.

Dr. Pedre: Oh, yes. This book went through– once I delivered the final manuscript, and I worked with a private editor, we refined each chapter multiple, multiple times. Then my main editor took everything and turned it upside down. The book was re-edited three or four– actually, no, four times, but each time, I could feel the book getting better and better. It was just like refinements, refinements.

Honestly, it’s a painful process, but it’s a very necessary process to be able to put a message out there that is as crystal clear as possible for anyone that doesn’t have science knowledge to be able to read it and understand the science behind, in my case, gut health. For you, it’s energy metabolism, mitochondria. They are interrelated anyway. It’s one of those journeys. I think of it as like Jesus’ 40 days in the desert.

You’re parched, you don’t know where the water is, you’re looking for an oasis, and you’re just riding and riding and riding.

Ari: I saw a meme yesterday posted by– I think it was posted by one of our friends, Isabella Wentz. It was a cartoon depiction, but it was people who read at the top, and it was people looking very refined and sophisticated, and their appearance done up. Then below that was people who write, and it was two people who look like they were homeless, disheveled, looked like they hadn’t showered or brushed their hair in five days, their beard all grown out in a horrible way.

Dr. Pedre: When I was going through book edits, I found this actually to be really useful. I use these– you’ve seen those large Post-its, the sticky ones?

Ari: Yes.

Dr. Pedre: I had my living room filled with Post-its, and I was writing all of the things that I had to move and shift and change in the book to keep it visually track of everything because when– I don’t know if you feel this way, but when I’m writing a book, it’s like my brain needs to know where everything is all at once because everything is connected to everything else. It’s as if you have a litter of 12 kids and you need to know exactly what each of them is doing at every single moment because if you say something here, it has to make sense over here, and you’ve got to make sure the order is right and all that. Anyway–

Ari: Yes, that’s smart.

Dr. Pedre: You know how much energy it takes to put a book together.

Gut health improvement is not a one size fits all approach

Ari: No question. Why did you put yourself through the torture of that? You wrote a book called Happy Gut just a few years ago, now you got another one called The GutSMART Protocol. Why another book? Has the science changed so much in the last few years that a new book became necessary, or what was the motivating factor here?

Dr. Pedre: It was the merits between where the science is going about gut health, and especially the gut microbiome, and also just my clinical experience working with patients with gut health issues. Again, always seeking to answer a problem that I think has not been addressed well enough in the open market. For this, it’s like a lot of the gut health books are eat more fiber, do this, but– it’s, everybody do the same thing.

What I found working through functional medicine, we personalize the approach for the patient. What I wanted and the idea I came up with is, how can I take my personalized approach and put it into a book that everybody can use and read so that you can have a program that fits you the best way that it can? Working with people with gut health issues, I realized that no two guts are the same, so their diet can’t be the same.

Ari: Okay. Now, there’s not going to be any more fluff or beating around the bush here because I’m going to ask you some hard-hitting questions starting right now. How can that be possible to do in the context of a book? I’ll tell you why based on my recent personal experience. I decided, six months ago or eight months ago, for the first time in my life to do some gut testing. Not out of any gut symptoms but, just more than anything, out of curiosity. I wanted to see what’s going on in my gut. I’m just interested in seeing what’s getting a window into what’s happening in my body. I went to a local functional medicine practitioner who could do some of these tests. A highly regarded practitioner.

Dr. Pedre: I wonder if I know him. [chuckles]

Ari: He’s highly regarded in San Diego, referred to me by a mutual friend of ours, JJ Virgin. For people listening, JJ is not the practitioner. She is a mutual friend who referred me to this person. He was going to order me a test for looking at insights into the gut microbiome. What I said was based on what I know in general about many functional medicine tests, is that many tests have limited degrees of accuracy, and many tests that use different technologies maybe sometimes arrive at different results.

What I said is, okay, let’s do the test you want to do, and I want you to also order me this other one with a different technology. The one that he wanted to order was a gut zoomer test from the, what’s the name?

Dr. Pedre: Vibrant?

Ari: Yes, Vibrant.

Dr. Pedre: Vibrant America.

Ari: It was the gut zoomer test, and I said, okay, let’s do that one, and I want you to order me this the Genova GI Effects.

Dr. Pedre: Yes, they give you– there’s overlap, but there’s also differences.

Ari: Yes. Anyway, I wanted to know for sure if a test is saying, hey, here’s what’s going on in your gut, that I have a second one saying, yes, this result is consistent across this other test too. What I found was almost no consistency. Literally, opposite findings of many key parameters. For example, high lactobacilli count on one, low lactobacilli count on the other; high bifidobacteria count on one, low on the other. Short-chain fatty acids. One said I’m super low in butyrate production, the other one said I’m sky high, in the 99th percentile as far as– off the charts as far as butyrate production.

Dr. Pedre: Now, I have a question.

Ari: Okay.

Dr. Pedre: Were these collected at the same time, same stool sample?

Ari: Same exact stool sample, of course.

Dr. Pedre: Same stool sample.

Ari: Same stool sample. 100%. I swear to you. I’m aware of that. Obviously, I ordered the two tests in advance. I made sure to take them with the same stool sample. Now, I talked to another one of my microbiome experts. You and one other guy who I consider absolutely top-notch named Jason Hawrelak. I had him look at the test, and he said, “Basically, there’s no conclusions we could draw from this because there’s very little matching.” He had me do a third test using a different technology, using a– I forget the name of the technology, but it’s like Whole-genome sequencing technology. It tells you all the species that are detectable in there.

Dr. Pedre: Which in itself can be a confusing thing.

Ari: Right. Itself is limited in the whole story that it tells you. Now I have three gut tests. Admittedly, the third one was not the same stool sample, but also now clear differences, not matching up, maybe matching up sometimes with one, not matching up with the other. To some extent, I’m like, okay, well, what do I do with–? I’ve done three tests, which have given me this huge amount of data, and yet I’m not sure what to even do with all of this data because I don’t know how much stock I can put into the conclusions.

Anyway, all of this is to say how difficult it must be to accurately personalize gut health recommendations, gut protocols to someone with or without [laughs] gut testing and microbiome testing.

Dr. Pedre: Even—

Ari: Tell me how you conceptualize that landscape,

Dr. Pedre: Even with gut testing, I always have viewed that caring for patients is like putting an interlay of transparencies. The old transparencies, you could put one on top of the other when you were with the teacher and they would draw something and then add it on top. Then what’s projected is the final result. I always think of working with patients is like putting together their story, and then on top of their story, I’m going to do some data collection. Then maybe there’s blood work, and then on top of that blood work, maybe there’s gut testing, maybe there’s some other blood markers that I’m going to look at.

I’m going to put all of it together and then look at the person as a whole and always trust the story that the person is telling me and the symptoms that they’re feeling over the test. You’re always deciding, who do I trust more? Do I trust the test? Do I trust the person? How do I synthesize all of this information knowing that there can be certain inaccuracies?

Really, if you look at the quiz, the GutSMART quiz in my book, it’s not a test. It’s not an objective test where you could say these are objective tests. It’s a quiz that’s asking the person to go through an array of symptoms that are either in the gut or related to the gut because we know there are these gut-related health issues from skin, brain, metabolism, all that. I go through a series of questions, created a score out of that, you get a number score from 25 to 450, and then within that number score, you get a qualitative score, you’re mild, moderate, or severe.

What I did is I then looked at a lot of science on food list, FODMAP diet, all that, divvied up, spoke with leading fermentationist, you know her, Summer Bock, to figure out, where did the ferments lie, and how much can they eat if they’re this or that? I came up with a really extensive– probably if you open it, you’ll see the most extensive food list broken down by mild, moderate, and severe.

Then I also try to teach people that you’ve got to be your own health guru. I want them to learn intuition, to really start tuning into the body, to become embodied and connected with their bodies, to start tuning into, how does food affect you? There’s so many intricacies. We even know like in SIBO patients, one’s going to do horrible with avocado, another one can have a third of an avocado and is fine. There are all these intricacies.

You know what I want to bring in, because I want to turn this whole thing upside down? Let’s just assume now that the Western gut is predominated when it’s healthy by butyrate-producing bacteria, which, by the way, are butyrate producers. Some of them are clostridia, which we usually associate as bad, but there are some good clostridia that are producing butyrate in the gut. For people who are listening, butyrate is a postbiotics metabolite that’s produced in the gut that feeds the colon cells but also helps balance blood sugar. It’s a histone deacetylase inhibitor, so it helps with learning and memory, production of BDNF.

The Hadza tribe has a vastly different microbiome from the typical Westerner

Now, as part of the research for this book, I went to Africa and I stayed with the Hadza, one of the last hunter-gatherers on the planet. I basically visited a human time capsule of what our human evolution has been for 95% of our time on Earth. We’ve been hunter-gatherers for 95% of history. We’ve been domesticating animals and growing mass agriculture for only 5% of that history. You look at their gut and– You could argue. You can say the testing, whatever, but if they use the same test, at least we can say they looked at a group of Hadza and they compared it to an Italian control group. The gut microbiome is not the same.

Ari: Meaning the gut microbiome in healthy Hadza hunter-gatherers is very, very different from healthy Western Italians.

Dr. Pedre: Yes. Western Italian control, which you would think are– the age range was about age-matched. I think the average age was around 32, but it ranged anywhere from the teens to 70. You have to think Italians are eating a pretty– the Westernized diet, but they’re in Italy eating a Mediterranean diet, lots of olive oil, so one of the healthiest diets, let’s say.

Ari: Certainly, much healthier than the typical American.

Dr. Pedre: Yes, exactly. The Hadza’s metabolome, so the postbiotics that are being produced by their gut microbiome, very different. Instead of butyrate being the predominant postbiotics, it’s propionate. There’ve been studies that’s connecting pronate with autism, saying propionate is not good, and yet here we have the Hadza, they have no diabetes, no obesity, no cardiovascular disease, no cancer. They’re a pretty healthy bunch.

Ari: This adds another element of complexity into the story that I told about myself and my own tests as well because the parameters given by the testing companies saying, “Hey, here’s what’s optimal. Here’s where you should be,” is determined by a sample of what population. A sample of presumably a Western population, not a sample of Hadza hunter-gatherers. We have to then understand– what I’m saying is maybe there’s cases where something it’s saying that, “Hey, your propionate or your butyrate levels are such and such, and they’re actually too low or too high relative to this sample of Westerners, but maybe they’re actually appropriate for, let’s say a hunter-gatherer population.”

Dr. Pedre: Part of the thought here as to why their propionate is high is, because they are hunter-gatherers, they are naturally intermittent fasting because there are times when they’re out hunting, they’re not eating. There could be extended periods of time when they’re not eating and propionate ends up being a substrate in the liver for gluconeogenesis. The hypothesis was that maybe they need more of those propionate producers because they’re going through long periods of fasting where they need their body to just be able to sustain itself while the men are out for the hunt. The other really interesting thing about their microbiome was the differences in the makeup of the gut microbiome.

Ari: What were some of the key differences or patterns that you saw?

Dr. Pedre: This was one of the biggest ones, is the presence of Treponema in their gut. Now, for anybody listening, Treponema is a spirochete. Treponema pallidum is the spirochete that causes syphilis. The type of Treponema in their gut is actually one that could cause some sort of skin reaction. Like something very– like a weeping skin wound. It’s not the healthiest bug to have, and yet in the Hadza, it does nothing, but it is serving a purpose.

It turns out that Treponema makes enzymes that help break down xylene and cellulose plant fibers. Because their diet is 70% plants, 30% animals, the women eat a little bit more plants than the men. Interestingly, unlike other groups where you look at, are there any sex differences in the makeup of the microbiome, kind of the microbiome signature, usually, there aren’t because they’re eating about the same. In the Hadza, because there is a division of labor between them, the women are always staying in camp – they don’t go hunting – so they tend to eat more tubers from root vegetables, a bit more high fiber, so their gut actually has a little bit more Treponema than the men.

Ari: And less meat and honey because when the men go out and they harvest honey, they eat it all before they take it home. They can’t resist.

Dr. Pedre: I went hunting and foraging with them, and I ate a root vegetable that was just dug up from the ground. Maybe not the best thing to do when you’re in Africa, but hey. I also had foraged honey, which by the way, I think when people hear like, “Oh, they’re eating honey,” they’re not eating honey the way we think of honey, like coming in a bottle and it’s just a nice honey. No, they’re eating the honeycomb and the honey bees because they get stuck in there.

Now, before somebody thinks this is gross, because I did this because they were like, “Hey, here.” When you’re with the Hadza, you do as the Hadza do. These honeybees are like tiny little flies. They do not look like the types of honeybees that we see here. They’re really tiny. They’re getting a lot more nutrients by eating the honeycomb and everything with it.

Ari: Yes. Absolutely. Okay. Higher levels of Treponema and–

Dr. Pedre: And more plant-degrading microbiomes. You could argue that if we took a Westerner and we slowly converted their diet towards– like maybe made them into a hunter-gatherer that we know the microbiome will shift over time. I don’t think that–

This is a belief system in functional medicine that you’ve probably heard many, many times over. Eat the rainbow. The rainbow is what creates the richest array of nutrients for the gut microbiome, it’s going to create microbial diversity, and yet the diversity of the gut of the Hadza, much greater than the Western control group of the Italians, they’re eating, like just mentioned, forage honey, medium to small and sometimes large game animals, tubers, root vegetables, berries, and baobab fruit. Those berries are not very colorful. They’re toned down, not super bright like we’re used to in the West.

They’re not eating the rainbow and yet they’ve got quite a varied gut microbiome. I think that part of it is that they’re out in nature. They’re not using antimicrobials, they’re not getting exposed to antibiotics, they’re not washing their hands. They’re getting exposed to dirt in the natural world. I think that that is a huge unrecognized microbiome diversifier.

Ari: Absolutely. Were there any other patterns notable as differences between the Italians and the Hadza as far as lactobacilli, bifidobacteria, or any other major species of bacteria?

Dr. Pedre: Absolutely. Yes. Thanks for bringing that up. In the Hadza group, they looked at age 8 to, I think 71, and there was no presence, zero bifidobacteria. Normally, we associate bifidobacteria as being part of the healthy gut. The question was, and the researchers mentioned this and said, it would be interesting to go back and check the poop of a breastfeeding infant because we know that breast milk with human milk oligosaccharides feeds the gut and helps populate the gut with bifidobacteria infantis to see if bifidobacteria is present.

Then they asked the question, is this something just with the Hadza? They went around Africa, and they looked at other groups, maybe not quite hunter-gatherers, but living in a more primitive way, like very plant-forward, like not eating a lot of animal meats or other more Westernized sources of food. They found similar patterns where bifido tends to get lost. That was another big difference. I think in the Italians, they also have acinetobacter which was not found.

There were some pretty big differences, which I think tells us something. I think it tells us something really important. There is not one microbiome that is the perfect microbiome makeup that will create perfect health for humans. There are different microbiomes that can create health.

A healthy microbiome can reduce inflammation

Now, there are important things that need to happen in that microbiome that we know from studying centenarians and looking at their microbiomes and seeing, what is it? Because another thing is, studying longevity and looking at the microbiome of aging, and why do some people live to 100 and other people don’t? Is there a difference in their microbiome? I found at least one study where they were looking at centenarians. What they found was that they had a greater presence of let’s call them inflammation-fighting bacteria in the gut. They were able to shut down inflammation more easily than, say, an 80-year-old who has a conglomeration of inflammatory, Westernized issues.

Ari: Going back to what I was saying a minute ago about the way these tests are done and how they are determining. The makers of these tests are establishing where one should be at, what is the optimal range that’s associated with health. Doesn’t–?

Dr. Pedre: I don’t think we know enough.

The right way to use microbiome tests

Ari: Our understanding of this whole thing is still in its infancy, and we don’t even yet know what are the optimal ranges as far as what is an ideal microbiome.

Dr. Pedre: I use these tests obviously in my practice, and I use them as ways to get extra data that I then interlay with the patient, the blood work, all the data that I have. I’m not just looking at a gut test in isolation, I’m matching it with the patient.

Now, there are certain pieces of gut tests that can be really helpful like pancreatic elastase that stays pretty consistent through the gut, calprotectin, other inflammatory markers, eosinophil protein x. I just diagnosed a patient who had come in with elevated eosinophils, but quite dramatic in the blood work more so than I would expect from allergies, from environmental stuff. I told him, “Hey, we should look at a gut test?”

I think when you’re looking at it from that perspective where you’re asking it a very specific question, like, is there a parasite here? I know these tests are not perfect for that, but the beautiful thing was that the test correlated with what I saw in the blood work. There’s a thing that you can check in the stool called eosinophilic protein X, which is secreted by eosinophils, so the white blood cells that get activated with allergies but also parasites. That was high. Then he was positive for entamoeba, so he did have a parasite.

Now, you don’t always see that. I think also I’ve become quite conservative. I think in my early days, I was being very reactive to what I saw in the testing. As I’ve kind of matured and graduated, I’m more weighted about what I see. I’ll ask myself, is this true? Does this make sense with the patient or does not make sense? I see practitioners out there who will get whatever tests with their patients, whether it’s Genova GI Effects, the GI-MAP, and it lights up with all this stuff. Then they’re reacting. They’re like, “Oh, you’ve got an overgrowth of this and you’ve got this and that.”

I always go back to the patient and the story and make sure, does this connect with how they’re presenting, and how can we reestablish balance without going crazy and throwing antibiotics and all these things? There’s other ways to reestablish the ecosystem.

Gut related symptoms

Ari: Let me add something to this, going back to my personal story. Now, here’s an alternate scenario that I could have easily been in and would have easily been in had I not been also a health expert and a student of this field and taken many graduate-level courses in gut health and microbiome health. I know about these tests and all this stuff. I brought this atypical thing of saying, hey, I’ll do your test, but I also want to do this other one.

This alternate scenario is I’m a typical patient and I just do the test that this practitioner told me to do. Then we get the results back and we now sit down and we interpret all this very sciency-looking data. We’re assuming, looking at only that test, that all of this is perfectly accurate. Now, there’s a diagnosis made based on that. The diagnosis that he was going to give me based on that one test was that I had some moderate degree of Dysbiosis, and he was ready to prescribe me his standard sort of Dysbiosis protocol.

Literally, he wanted me to buy a protocol of taking natural antimicrobials. Basically, a treatment with Biocidin and a number of other natural antimicrobials and you would go through this kill phase and a repopulate phase based on the idea that I had dysbiosis, but then I had another test that countered all of the findings of the first test and a third test that said I had very good gut health.

Again, imagine this alternate scenario that would be typical of really anybody else where they did just the one test, and now they’re doing a whole protocol of antimicrobials and a whole gut system based on the idea that they had a thing. They had this particular diagnosis that they may not have even actually had. I wonder how unbelievably common that must be.

Dr. Pedre: You know what I would be curious, Ari? What your GutSMART quiz score is.

Ari: I don’t have any gut symptoms. That’s the other thing why I was like, “I’m not going to go subject my gut to a bunch of antimicrobials if I don’t even have symptoms there.” I’m just doing this out of curiosity.

Dr. Pedre: I think it’s important, not just about gut symptoms, but do you have any gut-related symptoms that might be triggered by the gut? Again, I think the skill of the functional medicine practitioner, the more advanced one, is to weed through the test and say, “Relevant, not relevant.”

Ari: Yes.

Dr. Pedre: “Relevant, Not relevant.” I’ll give you an example of a patient that I included in the book where she came in to see me because she was breaking out in hives. She had fatigue, she had migrating joint pains. Now, if you’re a practitioner and you hear migrating joint pains, what do you think?

Ari: Probably rheumatoid arthritis or Bartonella, or something like that.

Dr. Pedre: Yes, tick-borne.

Ari: Yes.

Dr. Pedre: Tick-borne illness.

Ari: Yes.

Dr. Pedre: Yes. She was lighting up all across the board with autoimmune antibodies, and the doctors wanted to put her on prednisone and biologics. They wanted to basically shut down her immune system. She came to see me and instead, the question I asked is, “Why is your immune system going haywire? What has been missed here”? It wasn’t a tick-borne, that was ruled out. We looked at the gut, and actually when I asked her about gut symptoms, normal bowel movements, no constipation, no diarrhea, no abdominal pain, no bloating. No, I’m fine there, completely fine. Actually, all of her symptoms were rooted in her gut.

Ari: Interesting.

Dr. Pedre: We got lucky. Again, sometimes these tests, things start to hint in one direction or another. She had blastocystis hominis, which, if you do an internet search, you’re going to find a lot of things saying, oh, this is benign. It’s considered to be a commensal pathogen, many people have it. Then if you do a PubMed search on blastocystis hominis, you’ll find that it increases intestinal permeability and this has been proven. Then she also had a yeast– she was overgrowing I think it was rhodotorula. It was a yeast organism.

She actually had come from India to the US, and I also find that when there’s a big change in the diet from other countries where they might be using, for example, more ancestral wheat, and now they’re eating the overprocessed dwarf wheat that we have here in the US, that causes a problem. I took her off of gluten and dairy, and even with just that, within the first month, her hives were down by 50%, and then by two months, the hives were gone. Treated the blastocystis, treated the yeast, fatigue disappeared, migrating joint pain’s gone. She also had some mental fog, I believe that also lifted.

Sometimes you have no gut symptoms, but you’re lighting up. You have all these other things that are saying, screaming gut, which is what I talk about in my book is all these gut-related symptoms that you can have without any underlying gut issues, but you will have something. Like you said, you have no gut symptoms, but you’re also a really healthy guy overall. I’m just conjecturing just from seeing you on your surfboard in Costa Rica or wherever you go.

Ari: [chuckles] I am.

Dr. Pedre: Probably when you answer the questions on my quiz which ask not just about the gut but about all these things that could be gut-related happening in other parts of your body, I’m going to guess that you’re going to get a really low score. I could be wrong.

Ari: I’m sure I would. Now, there’s a couple interesting things I want to mention linking up with what you just said. There was one thing that was consistent across all three of my tests, which is that I have low Akkermansia muciniphila. That was insightful because that’s, as you know, and I’m saying this for listeners, a keystone species that’s involved in gut barrier integrity. It was useful to know that I have very low levels of this keystone species that’s important for that so I started taking a probiotic for that.

Dr. Pedre: You know how else you can build it up?

Ari: Apple peels and polyphenols and things like that, but I’m already doing tons of that and my levels were still super low so I figured maybe I’ll try adding some Akkermansia probiotic. The other thing– [crosstalk]

Dr. Pedre: [unintelligible 00:36:02] thing to look into there, and this, I would have to look at the research but the supporting cross-feeding that happens between probiotic bacteria, so looking at a bacillus species as a way to support Akkermansia.

Ari: What do you mean by that?

Fermented foods for gut health may be better than fibers

Dr. Pedre: Because you know cross-feeding, so cross-feeding is when one bacteria produces a postbiotic product that then supports the other bacteria. This is very common in the ecosystem, and actually, I was looking at– there was a really key study that came out, not a perfect study, but it was a study put out by Stanford University back in 2021 when I was writing my book. The study looked at a high fiber diet versus a high fermented foods diet, and what the effect was on different measures of microbial diversity, as well as different blood measures of inflammation, including not just C-reactive protein, but looking at cytokine activation of macrophages.

Again, it was one of those things where you’re thinking fiber rich eat the rainbow, that’s certainly going to create microbial diversity in the gut. This was a 17-week study. They had very specific dietary recommendations for each group. The fiber-rich group was told to eat about five to eight servings of fiber per day, so fiber-rich vegetables. To put that in grams, the most of the people in the fiber-rich group were eating 12 to 20-some grams, and during the intervention, they increased it over four weeks, then got to a six week period when they kept it at that high level, and they went up to 40-some grams so they more than doubled, some of them.

For the high fermented foods group, they on average, before the intervention were having 0.4 serving per day, so 0.4 cup, and they had them increased to four to six servings per day. Sounds like a lot but they were getting a lot of it through vegetable brine drinks, so it’s easier to take in that amount, vegetable brine and yogurt. They looked at these two groups, it was 18 and 18 people in each group, and they measured different measures of microbial diversity. It turned out that it wasn’t the fiber-rich group that increased microbial diversity, it was the fermented foods group.

Ari: That increased [crosstalk] or they increased it more?

Dr. Pedre: They increased it much more, whereas the fiber-rich group was really interesting because then they decided to go back to the fiber rich group and see well, what happened with immunomodulation because the high fermented foods group increased microbial diversity and all of them lowered 19 inflammatory markers. They all dropped. We know that and I think sometimes there’s some debate around this, but I’ve come to the conclusion that microbial diversity is the holy grail regardless of what type of diversity it is because it could be a different diversity for the HADSA versus us. Microbial diversity is the holy grail for keeping inflammation down and being on antibiotics is the worst thing that you could do for microbial diversity.

They went back and looked at the fiber-rich group and they asked the question, well, are they all the same, and they found they actually weren’t the same. They split them into three groups. A low diversity group, a moderate diversity group, and a high microbial diversity group. They went back and just looked at the diversity of their gut microbiome. What they found was that if they had high diversity and they increased their fiber, that it actually had a positive effect on immune regulation, so it actually helped regulate, tone down the immune system. If they had low diversity with high fiber, it actually activated their immune system. It did different things depending on what gut microbial diversity was at baseline for those groups.

Ari: That explains, or it certainly is at least part of the explanation, why many people who have, for example, SIBO or who have other GI symptoms and signs of dysbiosis often complain when you add prebiotics and more fiber to their diet that they have more symptoms or their symptoms are getting worse. They feel worse when they include more fiber and more diversity of fibers.

Dr. Pedre: Yes. They have gut bugs in the wrong place and they’re fermenting those foods, that’s a whole complicated issue there, but yes. Now, I think if you’re looking at this and wondering, is it fiber? Is it ferment? What should we be eating? This is really damn confusing and I really do think– There was another study that I looked at that actually came out after my book was complete. It was a study done in– I think it was done in Ireland. Yes, it was done in Ireland. They took 45 people, they divided them into two groups, and they wanted to see what happens to a Perceived Stress Score, it’s the Cohen’s Perceived Stress Score, by putting people on a gut supportive diet versus not.

They did exactly what I would’ve wanted to do. They took fiber and ferments, they put them together in one group because I don’t think it’s one against the other. I think actually, if I went back and I was designing that other study, I would’ve probably had four groups in the study. Fiber rich ferment, high fermented foods, fiber and fermented foods, and a control group that’s eating just a regular diet. What they did here is in this stress study, is they looked at what are the effects of increasing fiber 5 to 8 or 6 to 8 servings per day. Ferments, not as many, 2 to 3 servings, and they also had grains in there, and then versus a group where they just gave them general dietary guidelines like avoid processed foods, don’t eat too much sugar, but they really didn’t give them any pointers on how much to increase their fiber and their fermented foods.

Then they did it for four weeks and then retested the Perceived Stress Score on these two groups without any other intervention. There was no mental health stuff going on. There was no other like mind body stuff like what I talk about in my book like breath work and meditation. The group that was on the dietary intervention dropped their stress score by 32%. Whereas the placebo group, let’s call them the placebo group or the control group, they dropped by 17% and it was significant enough to say there’s something that’s happening here and it’s happening through the microbiome that’s affecting the way the brain is operating probably through the vagus nerve, and they actually then decided well, they were smart enough to keep compliance reports on the patients. Within the diet group, they looked at who had the highest compliance, who had the lowest compliance, and it correlated higher compliance with the diet, greater drop in their stress score.

The most common things that damage the microbiome

Ari: Excellent. What do you think are some of the biggest problems in the modern world when it comes to damaging gut health in the microbiome? I’m also curious to hear your thoughts on how this ties into mitochondrial health. We know that there’s many different axis in the body. The gut is connected with basically everything. There’s a gut brain axis, there’s a gut skin axis, there’s a gut lung axis, there’s a gut immune axis, and there’s a gut mitochondria axis. What are some of the biggest things that damage gut health in the modern world, and how does this story tie into mitochondria?

Dr. Pedre: Let’s go first with the things that damage gut health. I mean, number one is antibiotics, and not just prescribed antibiotics because I know you live in San Diego and people just go across the border and get things at the pharmacy in Mexico that you don’t need a prescription for, and usually, that includes like, oh, let me stock up on antibiotics for when I have a cold, so people are taking too many antibiotics and this is worldwide.

You can go to other countries, Asia, Southeast Asia, South America, where you can just walk into a pharmacy and get yourself an antibiotic and take it because you think you need an antibiotic when you actually just have a viral infection. Even CDC has looked at the prescription of antibiotics in the US, which is in the millions, and probably 20% to 30% of those prescriptions are unnecessary.

Ari: I’ll tell you being down here in Costa Rica, actually, I live in Costa Rica now, from San Diego, though. I think they’re like 30 years behind even States as far as thinking around this topic and there doesn’t seem to be any incorporation around knowledge of gut health and the microbiome and they prescribe antibiotics here like candy. I mean, just in the friends that I have here that are Ticos that are Costa Ricans, it seems like every little problem that they have, they’re like, here are some antibiotics. Here are some antibiotics. I’m like, are they giving antibiotics out here for everything? Good God. I think here, certainly, 20% to 30% of them being unnecessary, it’s probably more like 60% or 70%.

Dr. Pedre: Yes, and look, I went and trained as a Western doctor and I understand the thinking. I also know how antibiotics can save lives but I also understand the damage that antibiotic does to the gut, and the long-term effects that that can lead to over time. Again, just looking at the HADSA and seeing what happens if we don’t introduce antibiotics to the gut and the balance in the body.

Antibiotics are huge but there are so many other things that are indolent that you don’t see, you don’t smell; pesticides, glyphosate. I’ll use an example of a patient of mine recently, he lives in LA, between LA and Colorado, but he’s a pilot so sometimes he’s traveling, and at home, if you looked at him if I just had you, I would not tell you anything and just say, look at this person and tell me do they look healthy? You’d say they look healthy. A bit muscular, young looking, younger than his age, and eats organic at home, intermittent fasts, does all the right things, but when he travels, he might pick up some things along the way. Sometimes not eating quite along the organic diet plan that exists at home with his wife.

Because he’s a pilot, because he’s exposed to a lot of different chemicals, we did an environmental toxicity panel and I was shocked. I was not expecting this. His glyphosate level was off the charts high. His exposure didn’t seem like it was that much but it was significant enough. Why are we concerned? Not just that glyphosate is now a potential carcinogen, but also it is a disrupter. It’s a gut disrupter. It’s a chelating agent that binds minerals, and it actually works as an antimicrobial, so it’s almost like taking an antibiotic.

A lot of wheat in the US is contaminated with glyphosate, as well as soy and corn. Most of the soy and corn in the US is genetically modified and sprayed with glyphosate. It’s round-up-ready corn, which is resistant to glyphosate, so we have to think about those important gut disruptors. Alcohol, man, I hate to say it, but alcohol is a huge gut disruptor. Now, we know that alcohol, there’s always the argument, is a little drink okay? What’s too much? What’s acceptable? If you’re healing the gut, you can’t have your drink and heal your gut too. You just can’t do that. You’re cheating yourself if you think you can do that.

Oh, I’ll do the diet, I’ll do everything else right, but I’m not going to give up my wine. Well, let me break it to you. You’re not going to heal your gut. It’s not just the sugar and the alcohol, it is the alcohol itself, which is a disinfectant so it’s affecting the microbial ecosystem in your gut and then it’s increasing gut permeability, and then it’s increasing all sorts of inflammatory signals in your body. It’s feeding forward into that vicious cycle. Too much sugar in the diet, processed foods, the inflammatory seed oils, all of these things are big gut disruptors.

Even some of the things in our health food that might not be great for people like added gorgon, xanthan gum. It’s okay for some people, not so great for other people. That’s why I created– I teamed up with a chef for my book and some of the recipes, like we have a preservative-free almond milk that you can make at home, or preservative-free macadamia milk, super easy to make. If you’re really sensitive to these things like xanthan gum, it’s a prebiotic, gorgon might not sit well with you if you’ve got some bacterial overgrowth. It’s going to make you bloated and not feel great.

These are some of the big gut disruptors, along with things that people just pick up over-the-counter like NSAIDs and even acetaminophen. I found a study that showed that acetaminophen affects the makeup of the gut microbiome. We used to think NSAIDs, you got to be careful. They’ve been shown to increase gut permeability so they can lead to leaky gut. Then food sensitivities and whatnot. We know that too many NSAIDs could eat a hole in your stomach, cause an ulcer, but acetaminophen was generally thought of as gut-friendly, not liver friendly, but gut-friendly and I found at least one study that showed that it isn’t and it causes dysbiosis then leads to leaky gut and can lead to–

If you’re taking these over-the-counter seemingly benign medications or antacid medications like PPIs, the second most prescribed medication on the planet worldwide, proton-pump inhibitors. The blocking stomach acid which changes the ecosystem upstream and it causes this domino effect through the entire ecosystem. Again, another really important indolent gut disruptor that is available over the counter. Even if it’s not available over the counter, doctors will– I’ve seen doctors just keep prescribing it over and over to patients. These medications weren’t meant to be used for years on end and yet I’ve seen people who have been on them for 6, 8, 10 years.

Ari: It’s interesting to think of just how many of the problems that exist out there, health problems exist due to other medicines, other man-made medications that are supposed to combat some other problem, and then have these unintended consequences in other areas. Then we’ve got to deal with those problems and if you go see a conventional doctor, you’re probably going to get other drugs to treat those symptoms. Then more drugs and more drugs and more drugs.

Dr. Pedre: Who’s been to a psychiatrist and been given a medication to treat anxiety and then it causes a side effect, and the psychiatrist says, “Oh, no, don’t worry, I’ll give you this other medication to counter the side effect of that medication.” That new medication causes a side effect. They give you a third medication to counter the side effect of the second medication that’s countering the side effect of the first medication, when all you could be doing is working on gut health, improving gut health, and working on that gut-brain connection and you can get so far with that.

Ari: Yes. I spent some time working in internal medicine ward where it was common to see patients in their 60s, 70s, 80s who were on 12 or 15, or 18 different prescription drugs. The idea that this is “evidence-based medicine” is really absurd when you realize there isn’t a single study in existence in any humans where they’re taking that combination of those 12 or 15 different drugs together. As if any researcher or any physician actually knows about all of the total effects of all of these interactions between altering the systems with so many different drugs at the same time.

Do SSRIs have an effect on the gut microbiome and is that possibly part of the reason for their effects?

Dr. Pedre: By the way, if you don’t ask the question and research it, it doesn’t mean it doesn’t exist.

Ari: What do you mean?

Dr. Pedre: Recently, they asked the question, do antidepressants, do SSRIs have an effect on the gut microbiome and is that possibly part of the reason for their effects?

Ari: Ah, interesting.

Dr. Pedre: They found that they do, they’re just starting to figure this out, that they do have some effect that causes shifts in the gut microbiome. Now, we know from a study that came out at the end of December of last year, I think it was in Nature, they looked at over a thousand people in the Netherlands and they wanted to see is there a microbial signature for depression. They found that in the study, they looked at people who were depressed, there was a difference in their gut microbiome.

Now, let’s put a caveat here. Like you just said, if they did three different stool tests, maybe they would’ve had different results, but they found certain trends and there was a difference in 13 different taxa. The overriding conclusion was that the types of bacteria present in those that were depressed were associated with increases in inflammation in the body, or inability to regulate inflammation in different ways.

Ari: Super, super interesting. When you start to realize how many thousands and thousands of examples there are of similar kinds of things, you realize that we’re still in the Stone Ages. We think what we’re doing is so sophisticated and so evidence-based, but we’re tinkering with systems that we have a very surface-level understanding of and then we experience all kinds of unintended side effects like we described.

Dr. Pedre: I think I put this analogy in the book and it’s who’s the puppeteer? Are we the puppeteer or we the puppet or is the micro– and I think the microbiome is the puppeteer and we’re the puppets.

Ari: Interesting.

The connection between the gut and insulin sensitivity

Dr. Pedre: Because we used to think diabetes is a pancreas thing, it’s just a body phenomenon. Now we know that the microbiome influences the way your insulin sensitivity in your blood sugar metabolism. It’s like we weren’t asking the question so we thought it didn’t exist, but we just weren’t asking the right questions.

Ari: Go into that a little further. What’s the research on that? This is how consuming let’s say processed food or refined sugar interacts with the microbiome in a way that alters the way that the body uses insulin?

Dr. Pedre: Or even insulin sensitivity in different tissues. We can simplify it. We can tie this back to the mitochondria as well. It all goes back to something causes a disturbance in the gut microbiome, so the ecosystem is disturbed, not a good way. We call this dysbiosis. That dysbiosis leads to a breakdown of the gut barrier, so it causes increase in intestinal permeability or leaky gut. The more your gut is leaky, the more inflammatory substances are going to get through.

Those include LPS, lipopolysaccharide, endotoxin from gram-negative bacteria, but you can also find bacteria in the bloodstream and bacterial DNA because bacteria like throwing DNA around and stuff and communicating with each other and picking up things from each other. That lipopolysaccharide, there’s receptors for lipopolysaccharide everywhere in the body; in the muscle tissue, in the liver, the pancreas, the brain, the hypothalamus. When that receptor, the toll-like receptor 4 is stimulated, it activates an inflammatory cascade.

Now, who’s really sensitive to inflammation in the body and oxidation are mitochondria. Once you have that floodgate going and you’ve got this feed-forward system, you just think about people in this world, they’re stressed, they’re eating comfort foods, they’re having processed foods, they’re having processed oils, they’re having a drink on the weekend or even during the weekday because you’re stressed and you want to escape, and you’re just creating this inflammatory machine that then is scrambling all the processes inside your body, including affecting your mitochondria’s ability to work properly.


Ari: Phytochemicals. The last time we spoke, six or eight months ago, whenever it was, you mentioned that you were working on a paper that was, to some extent, working on redefining the way we currently think about prebiotic fibers and phytochemicals. Things like polyphenols and flavonoids and things link into that.

Dr. Pedre: Being prebiotics.

Ari: Describe to people what that means.

Dr. Pedre: Normally, we associate prebiotics with undigestible carbohydrates or resistant starches, and that’s one type of prebiotic, but when that type of prebiotic gets fermented or gets metabolized by your gut microbiome, it produces gas, so it produces hydrogen, methane gas. For people who have small intestinal bacterial overgrowth, they can get really bloated with that. You need to do something. You want to introduce something that can help start restoring that mucus layer and that gut barrier with these people, but you’re damned if you do, damned if you don’t. You can’t increase fiber, but one thing that you can do, because it goes through a different pathway, is increase polyphenols and bioflavonoids.

Pomegranate extract and citrus bioflavonoids have been shown to help increase the production of mucus and improve the mucus layer and then improve the bacteria that live on that mucus layer and then help with leaky gut without causing gas production. It’s the solution for people who are bloated, you know they have leaky gut, you know they’re suffering from a lot of gut-related health issues, but you need to hack the system because you can’t– You know prebiotics are good, you know resistant starch might be good, but you just can’t get it in there just yet, so you go through the different route.

Ari: I have one last question for you. Feel free to give a succinct answer. I’m sure you could probably talk for a long time about it. It relates to all this discussion of phytochemicals in plant foods that we’ve talked about quite a lot here. That is that there are certain dietary gurus who have come out in recent years who are carnivore diet proponents who are saying things like, hey, while animals can run away from us, they have four legs and that’s their defense strategy. Plants don’t have the ability to run away, and so they evolved a defense strategy that’s about phytochemicals and the production of plant toxins.

Dr. Pedre: Yes, like lectins and alkaloids and things like that.

Ari: Yes, and even sulforaphane and curcumin and some of these other phytochemicals that are designed as insecticides and as toxins for herbivorous animals that might consume them to poison them and so on. Therefore, these plants are full of toxins, and since toxins are bad for you, therefore the plants are bad for you, plants are trying to kill you. You should avoid eating plant foods and eat only meat. This is the basic gist of this idea or some variation on that general logic. What is your perspective on this claim?

Dr. Pedre: I’m going to say that like anything else, and there’s caveats to this and there’s obviously ways that we’ve evolved over the ages to prepare plant-based foods to reduce their anti nutrients, their phytic acid, their lectin content, all of that, but I think also we need to think of those as hormetic stressors for the body. Again, if you look at hunter-gatherer populations, there’s going to be a mix of animal and plant, there’s not just going to be a completely carnivore-driven historical human group. I think even some of the carnivores are starting to allow some plant-based foods in their diets because they realize that it’s not good for you to not have plants. Even if you look at the tooth structure of humans, we’re omnivores. We’re meant to eat meat and vegetables if you’re open to that. Where do I want to go with this?

Ari: What about from a microbiome perspective? What are the consequences of avoidance of plant foods?

Dr. Pedre: I think they’re big because these plant-based fibers are– and even the bioflavonoids, they’re feeding the microbiome in a way that helps support our body. Very important ways. I have a friend who did the carnivore diet as an experiment for his autoimmunity and actually as autoimmunity flared while he was on the carnivore diet. By and large, I’m going to say that the carnivore diet is a sympathetic nervous system-charging diet and it’s not right for the majority of people. Because you really need a diet that supports more of a parasympathetic state. We’re already sympathetic overcharged. We need to be more in a parasympathetic relaxed state, not only to digest but also to be able to heal.

The GutSMART protocol

Ari: Got it. Are there any final words you want to say and let people know where they can buy your new book, The GutSMART Protocol, and tell people where they will get from it?

Dr. Pedre: The GutSMART Protocol [unintelligible 01:05:01]. They can find it anywhere where books are sold, Amazon, Barnes & Noble, et cetera. If they go to,, they can get a bunch of bonuses there. If they just want to dip their toes in the water, they can actually get a free chapter and check out what the book is about before taking the dive. They can also find the quiz there, they can take the quiz, find out what their GutSMART Score is, and I’m actually– we didn’t even get to this part, man, we could do a third series on this gut-brain, vagus nerve.

I have a whole section on breathwork and meditation. The cool thing is I teamed up with breathwork and meditation teachers and I got them– I did interviews with them where they guide us through those meditations and breathwork and I actually divided them into– you can watch the full video interview, so you get a lot of value from that. All this is free on the website or you can just listen to the audio of the meditation by itself and do the meditation. Because, I mean what’s better than being led on meditation or breathwork by the instructor themselves? All the instructions are in my book but to be able to do it, almost feel like it’s live. I put all those resources on the website and there’s a QR code in the book that links to those resources.

Ari: Beautiful. Thank you so much, my friend, for coming on the show for the second time. It was an absolute pleasure as usual and I look forward to part three discussing what you were just alluding to there. Thank you so much. I look forward to the next one.

Dr. Pedre: Thank you.

Show Notes

00:00 – Intro
00:30 – Guest Intro
05:38 – Gut health improvement is not a one size fits all approach
15:55 – The Hadza tribe has a vastly different microbiome from the typical Westerner
26:00 – A healthy microbiome can reduce inflammation
27:10 – The right way to use microbiome tests
30:00 – Gut related symptoms
37:47 – Fermented foods for gut health may be better than fibers
45:45 – The most common things that damage the microbiome
55:35 – Do SSRIs have an effect on the gut microbiome and is that possibly part of the reason for their effects?
57:57 – The connection between the gut and insulin sensitivity
1:00:40 – Prebiotics


Check out Dr. Pedre’s Gut Smart Protocol here:

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